Exploring the Binding Mechanism of GABA_B Receptor Agonists and Antagonists through in Silico Simulations

Abstract

GABA B is a G protein-coupled receptor that functions as a constitutive heterodimer composed of the GABA B1a/b and GABA B2 subunits. It mediates slow and prolonged inhibitory neurotransmission in the nervous system, representing an attractive target for the treatment of various disorders. However, the molecular mechanism of the GABA B receptor is not thoroughly understood. Therefore, a better description of the binding of existing agonists and antagonists to this receptor is crucial to improve our knowledge about G protein-coupled receptor structure as well as for helping the development of new potent and more selective therapeutic agents. In this work, we used the recent X-ray cocrystallization data of agonists (GABA and baclofen) and antagonists (2-hydroxysaclofen, SCH50911, and CGP54626) bound to the GABA B orthosteric site together with quantum biochemistry and the molecular fractionation with conjugate caps (MFCC) scheme to describe the individual contribution of each amino acid residue involved in the GABA B −ligand interaction, pointing out differences and similarities among the compounds. Our quantum biochemical computational results show that the total binding energy of the ligands to the GABA B ligand pocket, with radius varying from 2.0 to 9.0 Å, is well-correlated with the experimental binding affinity. In addition, we found that the binding site is very similar for agonists or antagonists, showing small differences in the importance of the most significant amino acids. Finally, we predict the energetic relevance of the regions of the five ligands as well as the influence of each protein lobe on GABA B −ligand binding. These results provide important new information on the binding mechanism of the GABA B receptor and should facilitate the development of new chemicals targeting this receptor.

The GABAB Receptor—Structure, Ligand Binding and Drug Development

“…Additional mutational studies followed by radioligand binding assays showed that mutating Ser130 to Ala abolished binding of the antagonist CGP54626, while mutation of Ser153 were found to affect the affinity of various ligands differently and are thereby suggested to play a role in selectivity of GABA B ligand recognition [51]. For more details about ligand interactions in the orthosteric binding site, please see [36,[51][52][53]. Ligand interactions with residues located in LB2 seem to be restricted to agonists and high-affinity antagonists [36,52,53].…”

“…For more details about ligand interactions in the orthosteric binding site, please see [36,[51][52][53]. Ligand interactions with residues located in LB2 seem to be restricted to agonists and high-affinity antagonists [36,52,53]. Interactions with residues in both LB1 and LB2 are likely to be a requirement for activation, and cause the agonists to become buried within the closed receptor conformation (Figure 3).…”

“…These studies have not succeeded in obtaining clinical compounds, but with available 3D structures of the full receptor, new possibilities are provided also for new orthosteric compounds. Most of the in silico studies have been a combination of ligand based and structure based methods to identify potential hits and explore the VFT mechanisms [52,53,111,112].…”

“…All ligands co-crystalized with the VFT are structural derivatives of GABA with an α-acid and a γ-amino group [ 36 ]. The α-acid and the γ-amino groups of co-crystalized ligands are stabilized by identical residual interactions in all X-ray crystal structures, independent of intrinsic ligand activity [ 36 , 52 , 53 ]. Linking receptor interaction patterns to ligand activity and affinity has proven to be difficult, as highly similar compounds show similar receptor interaction patterns despite of different activity [ 36 ].…”

Exploring the Spike-hACE 2 Residue–Residue Interaction in Human Coronaviruses SARS-CoV-2, SARS-CoV, and HCoV-NL63

“…Since the PROPKA software is slightly sensitive to the ligand pocket geometry, the steps of hydrogen addition/withdrawal and energy minimization are carried out until no difference is observed in the protonation results. 26 …”